Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
Schoch, Conrad L.1; Robbertse, Barbara1; Robert, Vincent2; Duong Vu2; Cardinali, Gianluigi3; Irinyi, Laszlo4; Meyer, Wieland4; Nilsson, R. Henrik5; Hughes, Karen6; Miller, Andrew N.7; Kirk, Paul M.8; Abarenkov, Kessy9; Aime, M. Catherine10; Ariyawansa, Hiran A.11,12; Bidartondo, Martin13; Boekhout, Teun2; Buyck, Bart14; Cai, Qing15; Chen, Jie11,12; Crespo, Ana2,16; Crous, Pedro W.2; Damm, Ulrike17; De Beer, Z. Wilhelm18; Dentinger, Bryn T. M.8; Divakar, Pradeep K.16; Duenas, Margarita19; Feau, Nicolas20; Fliegerova, Katerina21; Garcia, Miguel A.22; Ge, Zai-Wei15; Griffith, GarethW.23; Groenewald, Johannes Z.2; Groenewald, Marizeth2; Grube, Martin24; Gryzenhout, Marieka25; Gueidan, Cecile26; Guo, Liangdong27; Hambleton, Sarah28; Hamelin, Richard20; Hansen, Karen29; Hofstetter, Valerie30; Hong, Seung-Beom31; Houbraken, Jos2; Hyde, Kevin D.11,12; Inderbitzin, Patrik32; Johnston, Peter R.33; Karunarathna, Samantha C.11,12; Koljalg, Urmas9; Kovacs, Gabor M.34,35; Kraichak, Ekaphan36; Krizsan, Krisztina37; Kurtzman, Cletus P.38; Larsson, Karl-Henrik39; Leavitt, Steven36; Letcher, Peter M.40; Liimatainen, Kare41; Liu, Jian-Kui11,12; Lodge, D. Jean42; Luangsa-ard, Janet Jennifer43; Lumbsch, H. Thorsten36; Maharachchikumbura, Sajeewa S. N.11,12; Manamgoda, Dimuthu11,12; Martin, Maria P.19; Minnis, Andrew M.44; Moncalvo, Jean-Marc45,46; Mule, Giuseppina47; Nakasone, Karen K.48; Niskanen, Tuula41; Olariaga, Ibai29; Papp, Tamas37; Petkovits, Tamas37; Pino-Bodas, Raquel49; Powell, Martha J.40; Raja, Huzefa A.50; Redecker, Dirk51; Sarmiento-Ramirez, J. M.19; Seifert, Keith A.28; Shrestha, Bhushan52; Stenroos, Soili49; Stielow, Benjamin2; Suh, Sung-Oui53; Tanaka, Kazuaki54; Tedersoo, Leho9; Teresa Telleria, M.19; Udayanga, Dhanushka11,12; Untereiner, Wendy A.55; Dieguez Uribeondo, Javier19; Subbarao, Krishna V.32; Vagvoelgyi, Csaba37; Visagie, Cobus2; Voigt, Kerstin56,57; Walker, Donald M.58; Weir, Bevan S.33; Weiss, Michael59; Wijayawardene, Nalin N.11,12; Wingfield, Michael J.18; Xu, J. P.60; Yang, Zhu L.15; Zhang, Ning61; Zhuang, Wen-Ying27; Federhen, Scott1; Yang, YP (reprint author), Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Div & Biogeog East Asia, Menglun Township 650201, Yunnan, Peoples R China.;
AbstractDNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
KeywordInternal Transcribed Spacer Arbuscular Mycorrhizal Fungi Ribosomal Dna Interspecific Hybridization Sequence Analyses Species Complex Identification Evolution Barcode Life
Subject AreaMathematical & Computational Biology
Indexed BySCI
WOS IDWOS:000338579600001
Citation statistics
Document Type期刊论文
Corresponding AuthorYang, YP (reprint author), Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Div & Biogeog East Asia, Menglun Township 650201, Yunnan, Peoples R China.;
Affiliation1.Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD 20894 USA
2.CBS KNAW Fungal Biodivers Ctr, NL-3508 AD Utrecht, Netherlands
3.Univ Perugia, Dept Pharmaceut Sci Microbiol, I-06100 Perugia, Italy
4.Univ Sydney, Marie Bashir Inst Infect Dis & Biosecur, Mol Mycol Res Lab,Sydney Med Sch,Westmead Hosp, Westmead Millennium Inst,Ctr Infect Dis & Microbi, Westmead, NSW 2145, Australia
5.Univ Gothenburg, Dept Biol & Environm Sci, S-40530 Gothenburg, Sweden
6.Univ Tennessee, Knoxville, TN 37920 USA
7.Univ Illinois, Illinois Nat Hist Survey, Champaign, IL 61820 USA
8.Royal Bot Gardens, Jodrell Lab, Mycol Sect, Richmond TW9 3DS, Surrey, England
9.Univ Tartu, Nat Hist Museum, EE-51014 Tartu, Estonia
10.Purdue Univ, Dept Bot & Plant Pathol, W Lafayette, IN 47907 USA
11.Mae Fah Luang Univ, Inst Excellence Fungal Res, Chiang Rai 57100, Thailand
12.Mae Fah Luang Univ, Sch Sci, Chiang Rai 57100, Thailand
13.Imperial Coll London, Royal Bot Gardens, Richmond TW9 3DS, England
14.Museum Natl Hist Nat, Dept Systemat & Evolut CP39, UMR7205, F-75005 Paris, France
15.Chinese Acad Sci, Kunming Inst Bot, Kunming 650201, Yunnan, Peoples R China
16.Univ Complutense Madrid, Fac Farm, Dept Biol Vegetal 2, E-28040 Madrid, Spain
17.Senckenberg Museum Nat Hist Gorlitz, D-02806 Gorlitz, Germany
18.Univ Pretoria, Dept Microbiol & Plant Pathol, FABI, ZA-0001 Pretoria, South Africa
19.CSIC, RJB, E-28014 Madrid, Spain
20.Univ British Columbia, Fac Forestry, Dept Forest & Conservat Sci, Vancouver, BC V6T 1W5, Canada
21.Acad Sci Czech Republic, Inst Anim Physiol & Genet, Vvi, Prague, Czech Republic
22.Univ Toronto, Dept Biol, Mississauga, ON L5L 1C6, Canada
23.Prifysgol Aberystwyth, Inst Biol Environm & Rural Sci, Aberystwyth SY23 3DD, Ceredigion, Wales
24.Karl Franzens Univ Graz, Inst Plant Sci, A-8010 Graz, Austria
25.Univ Orange Free State, Dept Plant Sci, ZA-9300 Bloemfontein, South Africa
26.CANBR, CSIRO Plant Ind, Canberra, ACT 2601, Australia
27.Chinese Acad Sci, Inst Microbiol, State Key Lab Mycol, Beijing, Peoples R China
28.Agr & Agri Food Canada, Biodivers Mycol & Microbiol, Ottawa, ON, Canada
29.Swedish Museum Nat Hist, Dept Bot, SE-10405 Stockholm, Sweden
30.Agroscope Changins Wadenswil Res Stn ACW, Dept Rech Protect Vegetaux Grandes Cultures & Vig, CH-1260 Nyon, Switzerland
31.RDA, Korean Agr Culture Collect, Natl Acad Agr Sci, Suwon 441707, South Korea
32.Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA
33.Landcare Res, Auckland 1142, New Zealand
34.Eotvos Lorand Univ, Inst Biol, Dept Plant Anat, H-1117 Budapest, Hungary
35.Hungarian Acad Sci, Inst Plant Protect, Agr Res Ctr, H-1525 Budapest, Hungary
36.Field Museum Nat Hist, Chicago, IL 60605 USA
37.Univ Szeged, Fac Sci & Informat, Dept Microbiol, H-6726 Szeged, Hungary
38.ARS, Bacterial Foodborne Pathogens & Mycol Res Unit, USDA, Natl Ctr Agr Utilizat Res, Peoria, IL 61604 USA
39.Nat Hist Museum, N-0318 Oslo, Norway
40.Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA
41.Univ Helsinki, Dept Biosci, FIN-00014 Helsinki, Finland
42.US Forest Serv, USDA, NRS, Luquillo, PR USA
43.Natl Ctr Genet Engn & Biotechnol BIOTEC, Pathum Thani 12120, Thailand
44.Univ Wisconsin, Dept Med Microbiol & Immunol, Madison, WI 53706 USA
45.Univ Toronto, Royal Ontario Museum, Dept Nat Hist, Toronto, ON, Canada
46.Univ Toronto, Dept Ecol Evolutionary Biol, Toronto, ON, Canada
47.CNR, Inst Sci Food Prod, I-70126 Bari, Italy
48.US Forest Serv, Ctr Forest Mycol Res, No Res Stn, Madison, WI 53726 USA
49.Univ Helsinki, Finnish Museum Nat Hist, Bot Museum, FI-00014 Helsinki, Finland
50.Univ N Carolina, Dept Chem & Biochem, Greensboro, NC 27402 USA
51.Univ Bourgogne, Agroecol UMR1347, F-21000 Dijon, France
52.Sungkyunkwan Univ, Inst Life Sci & Biotechnol, Suwon 440746, South Korea
53.ATCC, Mycol & Bot Program, Manassas, VA 20110 USA
54.Hirosaki Univ, Fac Agr & Life Sci, Hirosaki, Aomori 0368561, Japan
55.Brandon Univ, Dept Biol, Brandon, MB R7A 6A9, Canada
56.Leibniz Inst Nat Prod Res & Infect Biol, Jena Microbial Resource Collect, Jena, Germany
57.Univ Jena, Jena, Germany
58.Univ Findlay, Dept Nat Sci, Findlay, OH 45840 USA
59.Univ Tubingen, Inst Evolut & Ecol, D-72076 Tubingen, Germany
60.McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada
61.Rutgers State Univ, Dept Plant Biol & Pathol, New Brunswick, NJ 08901 USA
Recommended Citation
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Schoch, Conrad L.,Robbertse, Barbara,Robert, Vincent,et al. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi[J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION,2014:bau061.
APA Schoch, Conrad L..,Robbertse, Barbara.,Robert, Vincent.,Duong Vu.,Cardinali, Gianluigi.,...& needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION,bau061.
MLA Schoch, Conrad L.,et al."Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi".DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2014):bau061.
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